Bioconductor Forum

Dear all, I'm using DiffBind to find the differentially methylated regions. Libraries have been obtained by using the Methyl-binding...Should I go for the background or the Reads in Peak (RiP) normalization? Are there some specific "rules" for the MBD-seq? I know, and it is clearly written in the manual, that there are many strategies and none is the perfect one

MBD-seq DiffBind

updated 16 months ago • Marianna

Hello all, I've been trying to install WGCNA on our cluster. It has module system, so I've chosen R-3.1.2 and installed bunch of libs locally...a>") biocLite("GO.db") </pre> <pre> it returned ----- (download, installation logs here, no errors) --------- ** testing if installed package can be loaded Error in sqliteSendQuery(con, statement, bind.data) : error in state…

go sqlite

updated 10.1 years ago • predeus

div class="preformatted">Hi Diana, the 'issue' you are seeing is due to the "True Path Rule". I suspect that the geneID2GO mappings gives only the specific annotation to a particular GO term. However during the...are pushed up the hierarchy. So a GO term will contain the genes specifically annotated to it plus all the genes present in the children (and it goes recursively). The root of the h…

Annotation GO topGO Annotation GO topGO

updated 12.4 years ago • Adrian Alexa

Hi all, anyone can help with the following from the ATACseqQC package: objs <- splitBam(bamfile, tags=tags, outPath=outPath, + txs...txs, genome=genome, + conservation=phastCons100way.UCSC.hg19) ERROR as follows: > [E::sam_parse1] unrecognized type N > [W::sam_read1] Parse error at line 26 > [E::sam_parse1] u…

ATACseqQC ATAC-seq error split bam file

updated 6.7 years ago • theodore.georgomanolis

div class="preformatted"> Apple MAC OS X 10.4 R version 2.3.1 Running biocLite() with groupName = "all" does yield an OS error "/Applications/R.app/Contents/Resources/sush: pipe error: Too many open files" Is it possible to close...files as the installation proceeds? > biocLite(groupName = "all", destdir = "/Volumes/KilroyHD/kilroy/Software/BioConductor") Running getBioC version 0.1.…

Cancer Breast Biobase AnnBuilder xcms Cancer Breast Biobase AnnBuilder xcms

updated 19.5 years ago • Steven McKinney

I would like to use R. I have seen some annotation packages for R but specifically I need ACMG rules for my SNPs. Is there a way to do it in R? Is there any Bioconductor packages that gives ACMG rules as annotations? Thank you

ACMG SNP

updated 3.5 years ago • hamza_karakurt

Hi all, Would you have a suggestion how to fix this error? peak.counts <- regionCounts(pe.bams, all.peaks, param=param) Error: BiocParallel...errors 1 remote errors, element index: 1 3 unevaluated and other errors first remote error: Error: position vector should be...1-based I found a similar error here: [https://support.bioconductor.org/p/9144941/#9148614]…

csaw

updated 2.8 years ago • Chris

div class="preformatted"> hi all i'm using the EBcoexpress package to analyze a series of 29 Tumor vs 29 Normal cancer microarray data. following the directions...in the pdf file i can create the first coexpression matrix with no errors, however, when i run the initializeHP() function (as decscribed in the package file) i get the following error: Error in mvnX...data = data, prior = prior):…

Microarray Cancer EBcoexpress Microarray Cancer EBcoexpress

updated 13.1 years ago • Guest User

I am one of the managers of a computing system that has a very restrictive set of outbound firewall rules but that does allow access to https://bioconductor.org/. Recently, one of our users reported an error accessing URL https...https://mghp.osn.xsede.org/ is not in our set of allowed external sites, that explains the user's error. Although we were able to provide this user a workaround, I want …